Re: [HCP-Users] SBref Distortion Correction

[Glasser, Matthew]

Hi Gaurav,

I think this probably needs to be escalated to Jesper, the author of
topup, as I¹m not sure why it isn¹t working as well with your GE data as
it typically does with our Siemens data.  He¹ll likely want your phase up
and phase down spin echo images and the acquisition parameters.  I don¹t
think the issue is the phase encoding direction, as we use AP/PA for a lot
of other stuff now (7T, 3T Prisma, etc).  The on other thing is if you¹ve
got artifacts in the image (e.g. ghosting) that can confuse topup (which
is essentially a specialized nonlinear registration algorithm).

Peace,

Matt.

On 5/29/15, 8:41 AM, "Gaurav Patel"  wrote:

>It seems to not have worked very well (image order Phase 2, Phase 1,
>Phase 2 blended with Phase 1):



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Re: [HCP-Users] SBref Distortion Correction

[Glasser, Matthew]

Okay, that sounds like things are producing the expected outputs.  As to
why the correction isn’t quite as good, you could check to see how
different the corrected spin echo images look.  These should give you an
idea of how well the distortion correction worked:

${StudyFolder}/${Subject}/${fMRIName}/DistortionCorrectionAndEPIToT1wReg_FL
IRTBBRAndFreeSurferBBRbased/FieldMap/PhaseOne_gdc_dc_jac.nii.gz
${StudyFolder}/${Subject}/${fMRIName}/DistortionCorrectionAndEPIToT1wReg_FL
IRTBBRAndFreeSurferBBRbased/FieldMap/PhaseTwo_gdc_dc_jac.nii.gz


Peace,

Matt.

On 5/26/15, 3:10 PM, "Gaurav Patel"  wrote:

>There are 6 files in the subject I am looking at, labeled Warpfield_01 to
>06, in additino to Warpfield.nii.gz.All have 3 volumes, with the 2nd
>volume having the fieldmap/brain image in each.  Warpfield images 4-6
>look much like the final Warpfield image, whereas Warpfield images 1-3
>appear to be roughly inverted versions of 4-6.  Would it help for me to
>attach the images in a separate email?  Thanks
>
>__
>  gaurav patel
>  gauravpa...@gmail.com
>  www.neurofreak.net
>
>
>
>
>On May 26, 2015, at 3:19 PM, Glasser, Matthew wrote:
>
>> Are there only two of those files?  It¹s not really possible for
>>WarpField
>> to have a warpfield in it (that looks like a field map with a vaguely
>> brain shape inside it) but for the WarpField_01 and Warpfield_02 not to
>> have any data in them (did you check all their volumes)?
>>
>> Peace,
>>
>> Matt.
>>
>> On 5/26/15, 10:57 AM, "Juan Sanchez" 
>>wrote:
>>
>>> Looking at the WarpFields in the
>>>
>>>DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/FieldMa
>>>p
>>> directory,
>>> the "WarpField" looks good and has data,
>>> The "WarpField_01" and "WarpField_02" are both empty
>>>
>>>
>>> 
>>> From: hcp-users-boun...@humanconnectome.org
>>> [hcp-users-boun...@humanconnectome.org] on behalf of
>>> hcp-users-requ...@humanconnectome.org
>>> [hcp-users-requ...@humanconnectome.org]
>>> Sent: Friday, May 22, 2015 5:24 PM
>>> To: hcp-users@humanconnectome.org
>>> Subject: HCP-Users Digest, Vol 30, Issue 26
>>>
>>> Send HCP-Users mailing list submissions to
>>>   hcp-users@humanconnectome.org
>>>
>>> To subscribe or unsubscribe via the World Wide Web, visit
>>>   http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>> or, via email, send a message with subject or body 'help' to
>>>   hcp-users-requ...@humanconnectome.org
>>>
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>>>   hcp-users-ow...@humanconnectome.org
>>>
>>> When replying, please edit your Subject line so it is more specific
>>> than "Re: Contents of HCP-Users digest..."
>>>
>>>
>>> Today's Topics:
>>>
>>>  1. Re: SBref Distortion Correction (Glasser, Matthew)
>>>  2. Re: SBref Distortion Correction (Gaurav Patel)
>>>  3. Re: SBref Distortion Correction (Glasser, Matthew)
>>>  4. Re: Unresolved: 13-volume mismatch between rsfMRI volumes and
>>> trigger file? (Greg Burgess)
>>>
>>>
>>> --
>>>
>>> Message: 1
>>> Date: Fri, 22 May 2015 19:00:51 +
>>> From: "Glasser, Matthew" 
>>> Subject: Re: [HCP-Users] SBref Distortion Correction
>>> To: Juan Sanchez ,
>>>   "hcp-users@humanconnectome.org" 
>>> Message-ID: 
>>> Content-Type: text/plain; charset="us-ascii"
>>>
>>> An HTML attachment was scrubbed...
>>> URL:
>>>
>>>http://lists.humanconnectome.org/pipermail/hcp-users/attachments/2015052
>>>2/
>>> 5afce578/attachment-0001.html
>>>
>>> --
>>>
>>> Message: 2
>>> Date: Fri, 22 May 2015 15:28:37 -0400
>>> From: Gaurav Patel 
>>> Subject: Re: [HCP-Users] SBref Distortion Correction
>>> Cc: "hcp-users@humanconnectome.org" 
>>> Message-ID: 
>>> Content-Type: text/plain; charset="utf-8"
>>>
>>> Hi Matt? Juan is working with me at Columbia to get the topups working
>>> with the HCP pipeline.  The echo spacing is the same in both scans, as
>>>is
>>> the geometry we believe, though we still need to confirm that. 

Re: [HCP-Users] SBref Distortion Correction

[Gaurav Patel]

There are 6 files in the subject I am looking at, labeled Warpfield_01 to 06, 
in additino to Warpfield.nii.gz.All have 3 volumes, with the 2nd volume 
having the fieldmap/brain image in each.  Warpfield images 4-6 look much like 
the final Warpfield image, whereas Warpfield images 1-3 appear to be roughly 
inverted versions of 4-6.  Would it help for me to attach the images in a 
separate email?  Thanks

__
  gaurav patel
  gauravpa...@gmail.com
  www.neurofreak.net




On May 26, 2015, at 3:19 PM, Glasser, Matthew wrote:

> Are there only two of those files?  It¹s not really possible for WarpField
> to have a warpfield in it (that looks like a field map with a vaguely
> brain shape inside it) but for the WarpField_01 and Warpfield_02 not to
> have any data in them (did you check all their volumes)?
> 
> Peace,
> 
> Matt.
> 
> On 5/26/15, 10:57 AM, "Juan Sanchez"  wrote:
> 
>> Looking at the WarpFields in the
>> DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/FieldMap
>> directory,
>> the "WarpField" looks good and has data,
>> The "WarpField_01" and "WarpField_02" are both empty
>> 
>> 
>> 
>> From: hcp-users-boun...@humanconnectome.org
>> [hcp-users-boun...@humanconnectome.org] on behalf of
>> hcp-users-requ...@humanconnectome.org
>> [hcp-users-requ...@humanconnectome.org]
>> Sent: Friday, May 22, 2015 5:24 PM
>> To: hcp-users@humanconnectome.org
>> Subject: HCP-Users Digest, Vol 30, Issue 26
>> 
>> Send HCP-Users mailing list submissions to
>>   hcp-users@humanconnectome.org
>> 
>> To subscribe or unsubscribe via the World Wide Web, visit
>>   http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>> or, via email, send a message with subject or body 'help' to
>>   hcp-users-requ...@humanconnectome.org
>> 
>> You can reach the person managing the list at
>>   hcp-users-ow...@humanconnectome.org
>> 
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of HCP-Users digest..."
>> 
>> 
>> Today's Topics:
>> 
>>  1. Re: SBref Distortion Correction (Glasser, Matthew)
>>  2. Re: SBref Distortion Correction (Gaurav Patel)
>>  3. Re: SBref Distortion Correction (Glasser, Matthew)
>>  4. Re: Unresolved: 13-volume mismatch between rsfMRI volumes and
>> trigger file? (Greg Burgess)
>> 
>> 
>> --
>> 
>> Message: 1
>> Date: Fri, 22 May 2015 19:00:51 +
>> From: "Glasser, Matthew" 
>> Subject: Re: [HCP-Users] SBref Distortion Correction
>> To: Juan Sanchez ,
>>       "hcp-users@humanconnectome.org" 
>> Message-ID: 
>> Content-Type: text/plain; charset="us-ascii"
>> 
>> An HTML attachment was scrubbed...
>> URL:
>> http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20150522/
>> 5afce578/attachment-0001.html
>> 
>> --
>> 
>> Message: 2
>> Date: Fri, 22 May 2015 15:28:37 -0400
>> From: Gaurav Patel 
>> Subject: Re: [HCP-Users] SBref Distortion Correction
>> Cc: "hcp-users@humanconnectome.org" 
>> Message-ID: 
>> Content-Type: text/plain; charset="utf-8"
>> 
>> Hi Matt? Juan is working with me at Columbia to get the topups working
>> with the HCP pipeline.  The echo spacing is the same in both scans, as is
>> the geometry we believe, though we still need to confirm that. The
>> warpfield images have no information in them that I can tell, as changing
>> the scaling of the display doesn't reveal anything.  Also the shimming
>> should be the same for all scans. The spin echo and gradient echo images
>> look like they have the same distortions after they've been rigidly
>> realigned, so we're a little puzzled as to why the topup procedure is
>> failing. Any help would be appreciated. Thanks!
>> 
>> _
>> gaurav patel
>> gauravpa...@gmail.com
>> www.neurofreak.net
>> 
>>> On May 22, 2015, at 3:00 PM, Glasser, Matthew 
>>> wrote:
>>> 
>>> It helps to reply to the previous e-mail chain so that all of the info
>>> on a question is in one place.
>>> 
>>> Are you sure that those warp fields don?t have data in them, just a bad
>>> scaling of the display?  I don?t think the issue is with the topup
>>> configuration (we?ve never had 

Re: [HCP-Users] SBref Distortion Correction

[Glasser, Matthew]

Are there only two of those files?  It¹s not really possible for WarpField
to have a warpfield in it (that looks like a field map with a vaguely
brain shape inside it) but for the WarpField_01 and Warpfield_02 not to
have any data in them (did you check all their volumes)?

Peace,

Matt.

On 5/26/15, 10:57 AM, "Juan Sanchez"  wrote:

>Looking at the WarpFields in the
>DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/FieldMap
>directory,
>the "WarpField" looks good and has data,
>The "WarpField_01" and "WarpField_02" are both empty
>
>
>
>From: hcp-users-boun...@humanconnectome.org
>[hcp-users-boun...@humanconnectome.org] on behalf of
>hcp-users-requ...@humanconnectome.org
>[hcp-users-requ...@humanconnectome.org]
>Sent: Friday, May 22, 2015 5:24 PM
>To: hcp-users@humanconnectome.org
>Subject: HCP-Users Digest, Vol 30, Issue 26
>
>Send HCP-Users mailing list submissions to
>hcp-users@humanconnectome.org
>
>To subscribe or unsubscribe via the World Wide Web, visit
>http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>or, via email, send a message with subject or body 'help' to
>hcp-users-requ...@humanconnectome.org
>
>You can reach the person managing the list at
>hcp-users-ow...@humanconnectome.org
>
>When replying, please edit your Subject line so it is more specific
>than "Re: Contents of HCP-Users digest..."
>
>
>Today's Topics:
>
>   1. Re: SBref Distortion Correction (Glasser, Matthew)
>   2. Re: SBref Distortion Correction (Gaurav Patel)
>   3. Re: SBref Distortion Correction (Glasser, Matthew)
>   4. Re: Unresolved: 13-volume mismatch between rsfMRI volumes and
>  trigger file? (Greg Burgess)
>
>
>------
>
>Message: 1
>Date: Fri, 22 May 2015 19:00:51 +
>From: "Glasser, Matthew" 
>Subject: Re: [HCP-Users] SBref Distortion Correction
>To: Juan Sanchez ,
>"hcp-users@humanconnectome.org" 
>Message-ID: 
>Content-Type: text/plain; charset="us-ascii"
>
>An HTML attachment was scrubbed...
>URL:
>http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20150522/
>5afce578/attachment-0001.html
>
>--
>
>Message: 2
>Date: Fri, 22 May 2015 15:28:37 -0400
>From: Gaurav Patel 
>Subject: Re: [HCP-Users] SBref Distortion Correction
>Cc: "hcp-users@humanconnectome.org" 
>Message-ID: 
>Content-Type: text/plain; charset="utf-8"
>
>Hi Matt? Juan is working with me at Columbia to get the topups working
>with the HCP pipeline.  The echo spacing is the same in both scans, as is
>the geometry we believe, though we still need to confirm that. The
>warpfield images have no information in them that I can tell, as changing
>the scaling of the display doesn't reveal anything.  Also the shimming
>should be the same for all scans. The spin echo and gradient echo images
>look like they have the same distortions after they've been rigidly
>realigned, so we're a little puzzled as to why the topup procedure is
>failing. Any help would be appreciated. Thanks!
>
>_
> gaurav patel
> gauravpa...@gmail.com
> www.neurofreak.net
>
>> On May 22, 2015, at 3:00 PM, Glasser, Matthew 
>>wrote:
>>
>> It helps to reply to the previous e-mail chain so that all of the info
>>on a question is in one place.
>>
>> Are you sure that those warp fields don?t have data in them, just a bad
>>scaling of the display?  I don?t think the issue is with the topup
>>configuration (we?ve never had to change that, despite using it on
>>scanners with different field strengths).
>>
>> It would be good to check on what I suggested in the previous response.
>> While it is undoubtably better to use a proper SBRef generated from the
>>MB sequence itself, it should still be possible to do what you are
>>doing.  It is important that using a rigid registration of the MB to the
>>SBRef results in a very precise alignment (the images should have
>>exactly the same distortion).
>>
>> Another question, do you know that your scanner used the same shim for
>>all the scans?
>>
>> Peace,
>>
>> Matt.
>>
>> From: Juan Sanchez 
>> Date: Friday, May 22, 2015 at 8:56 AM
>> To: "hcp-users@humanconnectome.org" 
>> Subject: [HCP-Users] SBref Distortion Correction
>>
>>
>> Let us clarify what we are doing exactly here. We are using spin-echo
>>images with alternating phase-encoding directions

Re: [HCP-Users] SBref Distortion Correction

[Juan Sanchez]

Looking at the WarpFields in the 
DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/FieldMap 
directory,
the "WarpField" looks good and has data,
The "WarpField_01" and "WarpField_02" are both empty



From: hcp-users-boun...@humanconnectome.org 
[hcp-users-boun...@humanconnectome.org] on behalf of 
hcp-users-requ...@humanconnectome.org [hcp-users-requ...@humanconnectome.org]
Sent: Friday, May 22, 2015 5:24 PM
To: hcp-users@humanconnectome.org
Subject: HCP-Users Digest, Vol 30, Issue 26

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You can reach the person managing the list at
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When replying, please edit your Subject line so it is more specific
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Today's Topics:

   1. Re: SBref Distortion Correction (Glasser, Matthew)
   2. Re: SBref Distortion Correction (Gaurav Patel)
   3. Re: SBref Distortion Correction (Glasser, Matthew)
   4. Re: Unresolved: 13-volume mismatch between rsfMRI volumes and
  trigger file? (Greg Burgess)


--

Message: 1
Date: Fri, 22 May 2015 19:00:51 +0000
From: "Glasser, Matthew" 
Subject: Re: [HCP-Users] SBref Distortion Correction
To: Juan Sanchez ,
"hcp-users@humanconnectome.org" 
Message-ID: 
Content-Type: text/plain; charset="us-ascii"

An HTML attachment was scrubbed...
URL: 
http://lists.humanconnectome.org/pipermail/hcp-users/attachments/20150522/5afce578/attachment-0001.html

------

Message: 2
Date: Fri, 22 May 2015 15:28:37 -0400
From: Gaurav Patel 
Subject: Re: [HCP-Users] SBref Distortion Correction
Cc: "hcp-users@humanconnectome.org" 
Message-ID: 
Content-Type: text/plain; charset="utf-8"

Hi Matt? Juan is working with me at Columbia to get the topups working with the 
HCP pipeline.  The echo spacing is the same in both scans, as is the geometry 
we believe, though we still need to confirm that. The warpfield images have no 
information in them that I can tell, as changing the scaling of the display 
doesn't reveal anything.  Also the shimming should be the same for all scans. 
The spin echo and gradient echo images look like they have the same distortions 
after they've been rigidly realigned, so we're a little puzzled as to why the 
topup procedure is failing. Any help would be appreciated. Thanks!

_
 gaurav patel
 gauravpa...@gmail.com
 www.neurofreak.net

> On May 22, 2015, at 3:00 PM, Glasser, Matthew  wrote:
>
> It helps to reply to the previous e-mail chain so that all of the info on a 
> question is in one place.
>
> Are you sure that those warp fields don?t have data in them, just a bad 
> scaling of the display?  I don?t think the issue is with the topup 
> configuration (we?ve never had to change that, despite using it on scanners 
> with different field strengths).
>
> It would be good to check on what I suggested in the previous response.  
> While it is undoubtably better to use a proper SBRef generated from the MB 
> sequence itself, it should still be possible to do what you are doing.  It is 
> important that using a rigid registration of the MB to the SBRef results in a 
> very precise alignment (the images should have exactly the same distortion).
>
> Another question, do you know that your scanner used the same shim for all 
> the scans?
>
> Peace,
>
> Matt.
>
> From: Juan Sanchez 
> Date: Friday, May 22, 2015 at 8:56 AM
> To: "hcp-users@humanconnectome.org" 
> Subject: [HCP-Users] SBref Distortion Correction
>
>
> Let us clarify what we are doing exactly here. We are using spin-echo images 
> with alternating phase-encoding directions in alternating runs (Topup PA and 
> Topup AP, in  our case). We also decided to use the corresponding Topup (PA 
> or AP) as SBRef instead of an actual single-band reference image because we 
> had issues obtaining the single-band image and because the tissue contrast in 
> the spin-echo/Topup is pretty good (we tried using as SBRef the first frame 
> of the multiband EPI but the spin-echo/Topup definitely works better, 
> probably because of its improved tissue contrast). Even though using the 
> Topups instead of a B0 map for distortion correction and using the Topup as 
> SBRef instead of the first frame of the multiband EPI result in clear 
> improvements, the resulting undistorted SBRef is not perfectly aligned to the 
> anatom

Re: [HCP-Users] SBref Distortion Correction

[Gaurav Patel]

Hmmm...no I don't think so.  Will do and let you know

__
  gaurav patel
  gauravpa...@gmail.com
  www.neurofreak.net

> On May 22, 2015, at 3:32 PM, Glasser, Matthew  wrote:
> 
> Hi Gaurav,
> 
> Did you look at all 3 warpfield volumes (the second volume, Y, should contain 
> most of the info)?  
> 
> Peace,
> 
> Matt.
> 
> From: Gaurav Patel 
> Date: Friday, May 22, 2015 at 2:28 PM
> Cc: "hcp-users@humanconnectome.org" 
> Subject: Re: [HCP-Users] SBref Distortion Correction
> 
> Hi Matt… Juan is working with me at Columbia to get the topups working with 
> the HCP pipeline.  The echo spacing is the same in both scans, as is the 
> geometry we believe, though we still need to confirm that. The warpfield 
> images have no information in them that I can tell, as changing the scaling 
> of the display doesn't reveal anything.  Also the shimming should be the same 
> for all scans. The spin echo and gradient echo images look like they have the 
> same distortions after they've been rigidly realigned, so we're a little 
> puzzled as to why the topup procedure is failing. Any help would be 
> appreciated. Thanks!
> 
> _
>  gaurav patel
>  gauravpa...@gmail.com
>  www.neurofreak.net
> 
> On May 22, 2015, at 3:00 PM, Glasser, Matthew  wrote:
> 
>> It helps to reply to the previous e-mail chain so that all of the info on a 
>> question is in one place.  
>> 
>> Are you sure that those warp fields don’t have data in them, just a bad 
>> scaling of the display?  I don’t think the issue is with the topup 
>> configuration (we’ve never had to change that, despite using it on scanners 
>> with different field strengths).  
>> 
>> It would be good to check on what I suggested in the previous response.  
>> While it is undoubtably better to use a proper SBRef generated from the MB 
>> sequence itself, it should still be possible to do what you are doing.  It 
>> is important that using a rigid registration of the MB to the SBRef results 
>> in a very precise alignment (the images should have exactly the same 
>> distortion).  
>> 
>> Another question, do you know that your scanner used the same shim for all 
>> the scans?
>> 
>> Peace,
>> 
>> Matt.
>> 
>> From: Juan Sanchez 
>> Date: Friday, May 22, 2015 at 8:56 AM
>> To: "hcp-users@humanconnectome.org" 
>> Subject: [HCP-Users] SBref Distortion Correction
>> 
>> 
>> Let us clarify what we are doing exactly here. We are using spin-echo images 
>> with alternating phase-encoding directions in alternating runs (Topup PA and 
>> Topup AP, in our case). We also decided to use the corresponding Topup (PA 
>> or AP) as SBRef instead of an actual single-band reference image because we 
>> had issues obtaining the single-band image and because the tissue contrast 
>> in the spin-echo/Topup is pretty good (we tried using as SBRef the first 
>> frame of the multiband EPI but the spin-echo/Topup definitely works better, 
>> probably because of its improved tissue contrast). Even though using the 
>> Topups instead of a B0 map for distortion correction and using the Topup as 
>> SBRef instead of the first frame of the multiband EPI result in clear 
>> improvements, the resulting undistorted SBRef is not perfectly aligned to 
>> the anatomical images. For this reason, we think there's a problem with the 
>> procedures creating or applying the WarpField (the topup procedure or the 
>> applyward procedure that uses the WarpField to undistort the SBRef). The 
>> undistorted SBRef in an example subject from the HCP dataset looks 
>> noticeably better aligned to the anatomical image than ours. Furthermore, 
>> the WarpField.nii in that example subject looks very similar to the 
>> corresponding TopupField.nii (like a scaled version of it). In our data, in 
>> contrast, the TopupField.nii looks probably like it's supposed to look like 
>> (with some anatomical information) but the WarpField.nii is totally empty in 
>> some cases! After realizing this is the case, we think that our (main) 
>> problem may be in the topup procedure (or maybe the input images it uses or 
>> some later modification to the WarpField.nii). Could you give us any 
>> suggestions as to how to fix this issue? Maybe we need to adjust some of the 
>> configuration files that the topup procedure uses? Did you have to tweak any 
>> parameters to optimize this for your scanner? 
>> 
>> We're attaching one screencapture with the TopupField.nii and the 
>> WarpField.nii, another image showi

Re: [HCP-Users] SBref Distortion Correction

[Glasser, Matthew]

Hi Gaurav,


Did you look at all 3 warpfield volumes (the second volume, Y, should contain most of the info)?  


Peace,


Matt.




From: Gaurav Patel <gauravpa...@gmail.com>
Date: Friday, May 22, 2015 at 2:28 PM
Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] SBref Distortion Correction





Hi Matt… Juan is working with me at Columbia to get the topups working with the HCP pipeline.  The echo spacing is the same in both scans, as is the geometry we believe, though we still need to confirm that. The warpfield images have no information in
 them that I can tell, as changing the scaling of the display doesn't reveal anything.  Also the shimming should be the same for all scans. The spin echo and gradient echo images look like they have the same distortions after they've been rigidly realigned,
 so we're a little puzzled as to why the topup procedure is failing. Any help would be appreciated. Thanks!

_
 gaurav patel
 gauravpa...@gmail.com
 www.neurofreak.net


On May 22, 2015, at 3:00 PM, Glasser, Matthew <glass...@wusm.wustl.edu> wrote:




It helps to reply to the previous e-mail chain so that all of the info on a question is in one place.  


Are you sure that those warp fields don’t have data in them, just a bad scaling of the display?  I don’t think the issue is with the topup configuration (we’ve never had to change that, despite using it on scanners with different field strengths).  


It would be good to check on what I suggested in the previous response.  While it is undoubtably better to use a proper SBRef generated from the MB sequence itself, it should still be possible to do what you are doing.  It is important that using a rigid
 registration of the MB to the SBRef results in a very precise alignment (the images should have exactly the same distortion).  


Another question, do you know that your scanner used the same shim for all the scans?


Peace,


Matt.




From: Juan Sanchez <sanch...@nyspi.columbia.edu>
Date: Friday, May 22, 2015 at 8:56 AM
To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
Subject: [HCP-Users] SBref Distortion Correction







Let us clarify what we are doing exactly here. We are using spin-echo images with alternating phase-encoding directions in alternating runs (Topup PA and Topup AP, in
 our case). We also decided to use the corresponding Topup (PA or AP) as SBRef instead of an actual single-band reference image because we had issues obtaining the single-band image and because the tissue contrast in the spin-echo/Topup is pretty good (we tried
 using as SBRef the first frame of the multiband EPI but the spin-echo/Topup definitely works better, probably because of its improved tissue contrast). Even though using the Topups instead of a B0 map for distortion correction and using the Topup as SBRef
 instead of the first frame of the multiband EPI result in clear improvements, the resulting undistorted SBRef is not perfectly aligned to the anatomical images. For this reason, we think there's a problem with the procedures creating or applying the WarpField
 (the topup procedure or the applyward procedure that uses the WarpField to undistort the SBRef). The undistorted SBRef in an example subject from the HCP dataset looks noticeably better aligned to the anatomical image than ours. Furthermore, the WarpField.nii
 in that example subject looks very similar to the corresponding TopupField.nii (like a scaled version of it). In our data, in contrast, the
TopupField.nii looks probably like it's supposed to look like (with some anatomical information) but the
WarpField.nii is totally empty in some cases! After realizing this
 is the case, we think that our (main) problem may be in the topup procedure (or maybe the input images it uses or some later modification to the
WarpField.nii).
 Could you give us any suggestions as to how to fix this issue? Maybe we need to adjust some of the configuration files that the topup procedure uses? Did you have to tweak any parameters to optimize this for your scanner?



We're attaching one screencapture with
the TopupField.nii and the WarpField.nii, another image showing the T2 anatomical scan, and a third image showing the SBRef (Topup in our case).
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Re: [HCP-Users] SBref Distortion Correction

[Gaurav Patel]

Hi Matt… Juan is working with me at Columbia to get the topups working with the 
HCP pipeline.  The echo spacing is the same in both scans, as is the geometry 
we believe, though we still need to confirm that. The warpfield images have no 
information in them that I can tell, as changing the scaling of the display 
doesn't reveal anything.  Also the shimming should be the same for all scans. 
The spin echo and gradient echo images look like they have the same distortions 
after they've been rigidly realigned, so we're a little puzzled as to why the 
topup procedure is failing. Any help would be appreciated. Thanks!

_
 gaurav patel
 gauravpa...@gmail.com
 www.neurofreak.net

> On May 22, 2015, at 3:00 PM, Glasser, Matthew  wrote:
> 
> It helps to reply to the previous e-mail chain so that all of the info on a 
> question is in one place.  
> 
> Are you sure that those warp fields don’t have data in them, just a bad 
> scaling of the display?  I don’t think the issue is with the topup 
> configuration (we’ve never had to change that, despite using it on scanners 
> with different field strengths).  
> 
> It would be good to check on what I suggested in the previous response.  
> While it is undoubtably better to use a proper SBRef generated from the MB 
> sequence itself, it should still be possible to do what you are doing.  It is 
> important that using a rigid registration of the MB to the SBRef results in a 
> very precise alignment (the images should have exactly the same distortion).  
> 
> Another question, do you know that your scanner used the same shim for all 
> the scans?
> 
> Peace,
> 
> Matt.
> 
> From: Juan Sanchez 
> Date: Friday, May 22, 2015 at 8:56 AM
> To: "hcp-users@humanconnectome.org" 
> Subject: [HCP-Users] SBref Distortion Correction
> 
> 
> Let us clarify what we are doing exactly here. We are using spin-echo images 
> with alternating phase-encoding directions in alternating runs (Topup PA and 
> Topup AP, in  our case). We also decided to use the corresponding Topup (PA 
> or AP) as SBRef instead of an actual single-band reference image because we 
> had issues obtaining the single-band image and because the tissue contrast in 
> the spin-echo/Topup is pretty good (we tried using as SBRef the first frame 
> of the multiband EPI but the spin-echo/Topup definitely works better, 
> probably because of its improved tissue contrast). Even though using the 
> Topups instead of a B0 map for distortion correction and using the Topup as 
> SBRef instead of the first frame of the multiband EPI result in clear 
> improvements, the resulting undistorted SBRef is not perfectly aligned to the 
> anatomical images. For this reason, we think there's a problem with the 
> procedures creating or applying the WarpField (the topup procedure or the 
> applyward procedure that uses the WarpField to undistort the SBRef). The 
> undistorted SBRef in an example subject from the HCP dataset looks noticeably 
> better aligned to the anatomical image than ours. Furthermore, the 
> WarpField.nii in that example subject looks very similar to the corresponding 
> TopupField.nii (like a scaled version of it). In our data, in contrast, the 
> TopupField.nii looks probably like it's supposed to look like (with some 
> anatomical information) but the WarpField.nii is totally empty in some cases! 
> After realizing this is the case, we think that our (main) problem may be in 
> the topup procedure (or maybe the input images it uses or some later 
> modification to the WarpField.nii). Could you give us any suggestions as to 
> how to fix this issue? Maybe we need to adjust some of the configuration 
> files that the topup procedure uses? Did you have to tweak any parameters to 
> optimize this for your scanner? 
> 
> We're attaching one screencapture with the TopupField.nii and the 
> WarpField.nii, another image showing the T2 anatomical scan, and a third 
> image showing the SBRef (Topup in our case).
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> 
>  
> 
> The materials in this message are private and may contain Protected 
> Healthcare Information or other information of a sensitive nature. If you are 
> not the intended recipient, be advised that any unauthorized use, disclosure, 
> copying or the taking of any action in reliance on the contents of this 
> information is strictly prohibited. If you have received this email in error, 
> please immediately notify the sender via telephone or return mail.
> 
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Re: [HCP-Users] SBref Distortion Correction

[Glasser, Matthew]

It helps to reply to the previous e-mail chain so that all of the info on a question is in one place.  


Are you sure that those warp fields don’t have data in them, just a bad scaling of the display?  I don’t think the issue is with the topup configuration (we’ve never had to change that, despite using it on scanners with different field strengths).  


It would be good to check on what I suggested in the previous response.  While it is undoubtably better to use a proper SBRef generated from the MB sequence itself, it should still be possible to do what you are doing.  It is important that using a rigid
 registration of the MB to the SBRef results in a very precise alignment (the images should have exactly the same distortion).  


Another question, do you know that your scanner used the same shim for all the scans?


Peace,


Matt.




From: Juan Sanchez 
Date: Friday, May 22, 2015 at 8:56 AM
To: "hcp-users@humanconnectome.org" 
Subject: [HCP-Users] SBref Distortion Correction







Let us clarify what we are doing exactly here. We are using spin-echo images with alternating phase-encoding directions in alternating runs (Topup PA and Topup AP, in
 our case). We also decided to use the corresponding Topup (PA or AP) as SBRef instead of an actual single-band reference image because we had issues obtaining the single-band image and because the tissue contrast in the spin-echo/Topup is pretty good (we tried
 using as SBRef the first frame of the multiband EPI but the spin-echo/Topup definitely works better, probably because of its improved tissue contrast). Even though using the Topups instead of a B0 map for distortion correction and using the Topup as SBRef
 instead of the first frame of the multiband EPI result in clear improvements, the resulting undistorted SBRef is not perfectly aligned to the anatomical images. For this reason, we think there's a problem with the procedures creating or applying the WarpField
 (the topup procedure or the applyward procedure that uses the WarpField to undistort the SBRef). The undistorted SBRef in an example subject from the HCP dataset looks noticeably better aligned to the anatomical image than ours. Furthermore, the WarpField.nii
 in that example subject looks very similar to the corresponding TopupField.nii (like a scaled version of it). In our data, in contrast, the
TopupField.nii looks probably like it's supposed to look like (with some anatomical information) but the
WarpField.nii is totally empty in some cases! After realizing this
 is the case, we think that our (main) problem may be in the topup procedure (or maybe the input images it uses or some later modification to the
WarpField.nii).
 Could you give us any suggestions as to how to fix this issue? Maybe we need to adjust some of the configuration files that the topup procedure uses? Did you have to tweak any parameters to optimize this for your scanner?



We're attaching one screencapture with
the TopupField.nii and the WarpField.nii, another image showing the T2 anatomical scan, and a third image showing the SBRef (Topup in our case).
___
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The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended
 recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone
 or return mail.
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